Phoenix Wright's original print run was (I believe) 30,000 units. They shipped all of them, and 10,000 sold though in the first month (October), so Capcom figured their job was done, cancelled the game, and moved on.
It sold 5,000 in November, and another 10,000 in December, at which point the word-of-mouth on the game was really starting to spread (although it was positive from day-1). Especially after Christmas, when presents were opened.
The last 5,000 units were snapped up within the first few days of January, at which point the "shortage" became complete (although some people were having trouble finding the game long before then). Stores didn't order more units, because the game was cancelled, and they couldn't, so they just shrugged their shoulders and moved on. And Capcom was denying that there was a shortage or a need for a reprint, noting that it was "still selling" in January.
Then Capcom probably noticed that zero units were selling in February, or there was some sort of inter-division friction because of the threat of Americans storming the European launch of the game in March, because Capcom decided to un-cancel the game and do another print run.
I don't know how big the run was, but Capcom didn't advertise it's arrival, so most stores didn't order any copies, only the ones who were specifically pestering Capcom (or stores that kept up with videogame news) did, and yet the run still shipped out entirely.
NCSX got their copies on March 13, and the scattered stores that got copies probably got them on about the same day. I didn't see any local stores carrying the second run of the game, and most online stores who picked it up seemed to sell out in about a week. NCSX thought they had "several months" worth of supply, and they had it available longer than anyone else I know of, but they ran out as of yesterday, April 14.
NCSX is saying that a third run of the game has been produced, and will be arriving sometime next month.